Published in J Biopharm Stat on August 01, 2004
Semantic similarity in biomedical ontologies. PLoS Comput Biol (2009) 5.05
Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. BMC Bioinformatics (2008) 1.47
Semi-Automatically Inducing Semantic Classes of Clinical Research Eligibility Criteria Using UMLS and Hierarchical Clustering. AMIA Annu Symp Proc (2010) 1.33
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics (2010) 1.21
Fuzzy c-means clustering with prior biological knowledge. J Biomed Inform (2008) 1.05
Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures. BMC Bioinformatics (2008) 0.95
A shortest-path graph kernel for estimating gene product semantic similarity. J Biomed Semantics (2011) 0.93
Finding new genes for non-syndromic hearing loss through an in silico prioritization study. PLoS One (2010) 0.90
An integrative approach for measuring semantic similarities using gene ontology. BMC Syst Biol (2014) 0.89
A Review of Feature Selection and Feature Extraction Methods Applied on Microarray Data. Adv Bioinformatics (2015) 0.89
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis. BMC Bioinformatics (2007) 0.88
Semantic particularity measure for functional characterization of gene sets using gene ontology. PLoS One (2014) 0.86
HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins. PLoS One (2014) 0.86
Dynamically weighted clustering with noise set. Bioinformatics (2009) 0.84
An algorithm for finding biologically significant features in microarray data based on a priori manifold learning. PLoS One (2014) 0.84
Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data. BMC Syst Biol (2014) 0.81
Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering. Bioinformatics (2009) 0.80
GO-PCA: An Unsupervised Method to Explore Gene Expression Data Using Prior Knowledge. PLoS One (2015) 0.80
An improved method for functional similarity analysis of genes based on Gene Ontology. BMC Syst Biol (2016) 0.75
Identifying Significant Features in Cancer Methylation Data Using Gene Pathway Segmentation. Cancer Inform (2016) 0.75
SGFSC: speeding the gene functional similarity calculation based on hash tables. BMC Bioinformatics (2016) 0.75
Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI. PLoS One (2015) 0.75
Improving clustering with metabolic pathway data. BMC Bioinformatics (2014) 0.75
Semi-supervised clustering methods. Wiley Interdiscip Rev Comput Stat (2013) 0.75
Developing a similarity searching module for patient safety event reporting system using semantic similarity measures. BMC Med Inform Decis Mak (2017) 0.75
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res (2003) 14.37
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A (2008) 7.45
Nova regulates brain-specific splicing to shape the synapse. Nat Genet (2005) 6.58
The transcription factor Myc controls metabolic reprogramming upon T lymphocyte activation. Immunity (2011) 6.00
Genomics identifies medulloblastoma subgroups that are enriched for specific genetic alterations. J Clin Oncol (2006) 5.96
Subtypes of medulloblastoma have distinct developmental origins. Nature (2010) 5.94
Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics (2006) 5.59
Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays. Bioinformatics (2005) 5.01
Novel mutations target distinct subgroups of medulloblastoma. Nature (2012) 4.82
Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol (2006) 4.63
Genomic variation landscape of the human gut microbiome. Nature (2012) 4.38
CYP4F2 genetic variant alters required warfarin dose. Blood (2008) 4.23
Cross-species genomics matches driver mutations and cell compartments to model ependymoma. Nature (2010) 3.70
IL-35-mediated induction of a potent regulatory T cell population. Nat Immunol (2010) 3.43
Multistage nanoparticle delivery system for deep penetration into tumor tissue. Proc Natl Acad Sci U S A (2011) 3.34
Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci U S A (2003) 3.31
Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics (2003) 2.97
A transcriptomic analysis of the phylum Nematoda. Nat Genet (2004) 2.68
Algorithms for large-scale genotyping microarrays. Bioinformatics (2003) 2.66
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics (2006) 2.37
Can experiments in nonhuman primates expedite the translation of treatments for spinal cord injury in humans? Nat Med (2007) 2.29
A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility. Proc Natl Acad Sci U S A (2005) 2.19
The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res (2012) 2.18
A mouse model of the most aggressive subgroup of human medulloblastoma. Cancer Cell (2012) 2.15
Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol (2003) 2.10
Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice. J Virol (2009) 2.08
Adenovirus-mediated gene therapy with sitimagene ceradenovec followed by intravenous ganciclovir for patients with operable high-grade glioma (ASPECT): a randomised, open-label, phase 3 trial. Lancet Oncol (2013) 2.08
Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays. BMC Genomics (2004) 2.05
The draft genome of the parasitic nematode Trichinella spiralis. Nat Genet (2011) 2.03
NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. Bioinformatics (2004) 2.02
Stability and function of regulatory T cells is maintained by a neuropilin-1-semaphorin-4a axis. Nature (2013) 1.99
Shh pathway activity is down-regulated in cultured medulloblastoma cells: implications for preclinical studies. Cancer Res (2006) 1.90
Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins (2003) 1.84
Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Neuron (2012) 1.78
Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Res (2003) 1.75
Effects of pioglitazone and rosiglitazone on blood lipid levels and glycemic control in patients with type 2 diabetes mellitus: a retrospective review of randomly selected medical records. Clin Ther (2002) 1.72
Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med (2013) 1.66
A compilation of soybean ESTs: generation and analysis. Genome (2002) 1.62
Loss of epigenetic modification driven by the Foxp3 transcription factor leads to regulatory T cell insufficiency. Immunity (2012) 1.61
Organic anion transporting polypeptide 1B transporters modulate hydroxyurea pharmacokinetics. Am J Physiol Cell Physiol (2013) 1.56
Dopaminergic innervation of the human striatum in Parkinson's disease. Mov Disord (2005) 1.44
The need for resources for clinical research: the European Society of Cardiology calls for European, international collaboration. Lancet (2002) 1.41
12-O-tetradecanoylphorbol-13-acetate (TPA)-induced dual-specificity phosphatase expression and AML cell survival. Leuk Res (2005) 1.40
Developing a pathway for high-value, patient-centered total joint arthroplasty. Clin Orthop Relat Res (2013) 1.39
Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer. PLoS One (2010) 1.33
Involvement of hyaluronan in regulation of fibroblast phenotype. J Biol Chem (2007) 1.33
A mouse model of rhabdomyosarcoma originating from the adipocyte lineage. Cancer Cell (2012) 1.32
Hyaluronan facilitates transforming growth factor-beta1-mediated fibroblast proliferation. J Biol Chem (2008) 1.28
A novel multifunctional oligonucleotide microarray for Toxoplasma gondii. BMC Genomics (2010) 1.23
A mutation in separase causes genome instability and increased susceptibility to epithelial cancer. Genes Dev (2007) 1.23
The TLR2-MyD88-NOD2-RIPK2 signalling axis regulates a balanced pro-inflammatory and IL-10-mediated anti-inflammatory cytokine response to Gram-positive cell walls. Cell Microbiol (2008) 1.23
Splicing biomarkers of disease severity in myotonic dystrophy. Ann Neurol (2013) 1.22
H5N1 influenza virus pathogenesis in genetically diverse mice is mediated at the level of viral load. MBio (2011) 1.22
Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res (2004) 1.20
The consensus of the task force of the European Society of Cardiology concerning the clinical investigation of the use of autologous adult stem cells for repair of the heart. Eur Heart J (2006) 1.20
Longitudinal validation of a risk calculator for periodontal disease. J Clin Periodontol (2003) 1.18
The happy docs study: a Canadian Association of Internes and Residents well-being survey examining resident physician health and satisfaction within and outside of residency training in Canada. BMC Res Notes (2008) 1.17
A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations. Bioinformatics (2006) 1.17
Detecting cholangiocarcinoma in patients with primary sclerosing cholangitis. Gastrointest Endosc (2002) 1.16
Evaluation of local structure alphabets based on residue burial. Proteins (2004) 1.15
Hyaluronan facilitates transforming growth factor-β1-dependent proliferation via CD44 and epidermal growth factor receptor interaction. J Biol Chem (2011) 1.11
Preclinical models for neuroblastoma: establishing a baseline for treatment. PLoS One (2011) 1.09
A20-binding inhibitor of NF-κB (ABIN1) controls Toll-like receptor-mediated CCAAT/enhancer-binding protein β activation and protects from inflammatory disease. Proc Natl Acad Sci U S A (2011) 1.08
A polymeric sealant inhibits anastomotic suture hole bleeding more rapidly than gelfoam/thrombin: results of a randomized controlled trial. Arch Surg (2002) 1.08
Identification of transmembrane protein 88 (TMEM88) as a dishevelled-binding protein. J Biol Chem (2010) 1.06
Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. Genome Biol (2007) 1.06
The human hyaluronan synthase 2 (HAS2) gene and its natural antisense RNA exhibit coordinated expression in the renal proximal tubular epithelial cell. J Biol Chem (2011) 1.05
The plasticity of regulatory T cell function. J Immunol (2011) 1.03
Physicochemical and morphological characterisation of nanoparticles from photocopiers: implications for environmental health. Nanotoxicology (2012) 1.03
Limited contribution of the SPINK1 N34S mutation to the risk and severity of alcoholic chronic pancreatitis: a report from the United States. Dig Dis Sci (2003) 1.03
Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics (2005) 1.02
Three amino acid changes in PB1-F2 of highly pathogenic H5N1 avian influenza virus affect pathogenicity in mallard ducks. Arch Virol (2010) 1.02
Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages. Mol Biochem Parasitol (2004) 1.02
The sustainable farm families project: changing attitudes to health. Rural Remote Health (2009) 1.01
Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III. J Eukaryot Microbiol (2003) 1.01
Chemical genetic transcriptional fingerprinting for selectivity profiling of kinase inhibitors. Assay Drug Dev Technol (2007) 1.00
Sequence mining and transcript profiling to explore cyst nematode parasitism. BMC Genomics (2009) 1.00
Using motor behavior during an early critical period to restore skilled limb movement after damage to the corticospinal system during development. J Neurosci (2012) 0.98
Intestinal transcriptomes of nematodes: comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans. PLoS Negl Trop Dis (2008) 0.98
European variation in decision-making and parental involvement during preterm birth. Arch Dis Child Fetal Neonatal Ed (2014) 0.97
Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. BMC Evol Biol (2009) 0.97
Validity and accuracy of a risk calculator in predicting periodontal disease. J Am Dent Assoc (2002) 0.97
The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences. Mol Biochem Parasitol (2007) 0.96
NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics (2008) 0.96
RB1 gene inactivation by chromothripsis in human retinoblastoma. Oncotarget (2014) 0.96
Cross-species genomic and epigenomic landscape of retinoblastoma. Oncotarget (2013) 0.95
Retrospective study of total healthcare costs associated with chronic nonvalvular atrial fibrillation and the occurrence of a first transient ischemic attack, stroke or major bleed. Curr Med Res Opin (2009) 0.95
An expressed sequence tag analysis of the life-cycle of the parasitic nematode Strongyloides ratti. Mol Biochem Parasitol (2005) 0.94
Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation. BMC Genomics (2010) 0.93
Phase I study of decitabine with doxorubicin and cyclophosphamide in children with neuroblastoma and other solid tumors: a Children's Oncology Group study. Pediatr Blood Cancer (2010) 0.93
Early edema in warfarin-related intracerebral hemorrhage. Neurocrit Care (2007) 0.93
Nanoparticles from photocopiers induce oxidative stress and upper respiratory tract inflammation in healthy volunteers. Nanotoxicology (2012) 0.93
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biol (2006) 0.93
Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling. BMC Genomics (2009) 0.92